Electrical tunnel junctions consisting of alkanethiol molecules self-assembled on Au-coated Si substrates and contacted with Au-coated atomic force microscopy tips were characterized under varying junction loads in a conducting-probe atomic force microscopy configuration. Junction load was cycled in the fashion of a standard nanoindentation experiment; however, junction conductance rather than probe depth was measured directly. The junction conductance data have been analyzed with typical contact mechanics (Derjaguin-Muller-Toporov) and tunneling equations to extract the monolayer modulus ( similar to 50 GPa), the contact transmission ( similar to 2 x 10(-6)), contact area, and probe depth as a function of load. The monolayers are shown to undergo significant plastic deformation under compression, yielding indentations similar to 7 angstrom deep for maximum junction loads of similar to 50 nN. Comparison of mechanical properties for different chain lengths was also performed. The film modulus decreased with the number of carbons in the molecular chain for shorter-chain films. This trend abruptly reversed once 12 carbons were present along the backbone.